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[0, 0, 0.25, 1, 0.75, -2.088059005700416e-05, 0.6666666666666666, 0, 0, -9.791584346494995, -9.791584346494995],
[0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
[4.10882444652326, 1.000000000000001, 0.75, 6.163236669784885, 0.25, -9.130152198011388e-05, 0.6666666666666666, 0, 0, -10.67367787530101, -10.67367787530101],
[0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
[2.135333741579919, 1.033625318387959, 0.75, 3.098802395209587, 0.25, -0.0002115722735211989, 0.6666666666666666, 0, 0, -10.39556150666463, -10.3954971540729],
[0, 0, 0.25, 1, 0.75, -1.203269528105011e-05, 0.6666666666666666, 0, 0, -10.72451332270395, -10.72451332270395],
[0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
[0, 0, 0.25, 1, 0.75, -1.018317015066827e-05, 0.6666666666666666, 0, 0, -9.693499270494449, -9.693499270494449],
[2.135333741579919, 1.033625318387959, 0.75, 3.098802395209587, 0.25, -0.0002116121409017069, 0.6666666666666666, 0, 0, -10.42458266725845, -10.42451835962194],
[0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
[0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0],
[0, 0, 0.25, 1, 0.75, -3.644732584007215e-05, 0.6666666666666666, 0, 0, -10.99950027284604, -10.99730956113475]
]
},
"headers": [
["alpha;", "Synonymous substitution rate at a site"],
["β-", "Non-synonymous substitution rate at a site for the negative/neutral evolution component"],
["p-", "Mixture distribution weight allocated to β-; loosely -- the proportion of the tree evolving neutrally or under negative selection"],
["β+", "Non-synonymous substitution rate at a site for the positive/neutral evolution component"],
["p+", "Mixture distribution weight allocated to β+; loosely -- the proportion of the tree evolving neutrally or under positive selection"],
["LRT", "Likelihood ratio test statistic for episodic diversification, i.e., p+ > 0 and β+ > α"],
["p-value", "Asymptotic p-value for episodic diversification, i.e., p+ > 0 and β+ > α"],
["# branches under selection", "The (very approximate and rough) estimate of how many branches may have been under selection at this site, i.e., had an empirical Bayes factor of 100 or more for the β+ rate"],
["Total branch length", "The total length of branches contributing to inference at this site, and used to scale dN-dS"],
["MEME LogL", "Site Log-likelihood under the MEME model"],
["FEL LogL", "Site Log-likelihood under the FEL model"]
]
},
"analysis":{
"authors":"Sergei L. Kosakovsky Pond, Steven Weaver",
"citation":"Detecting Individual Sites Subject to Episodic Diversifying Selection. _PLoS Genet_ 8(7): e1002764.",
"contact":"spond@temple.edu",
"info":"MEME (Mixed Effects Model of Evolution)\n estimates a site-wise synonymous (α) and a two-category mixture of non-synonymous\n (β-, with proportion p-, and β+ with proportion [1-p-]) rates, and\n uses a likelihood ratio test to determine if β+ > α at a site.\n The estimates aggregate information over a proportion of branches at a site,\n so the signal is derived from\n episodic diversification, which is a combination of strength of selection [effect size] and\n the proportion of the tree affected. A subset of branches can be selected\n for testing as well, in which case an additional (nuisance) parameter will be\n inferred -- the non-synonymous rate on branches NOT selected for testing. Multiple partitions within a NEXUS file are also supported\n for recombination - aware analysis.\n ",
"requirements":"in-frame codon alignment and a phylogenetic tree",
"version":"2.1.2"
},
"branch attributes":{
"0":{
"epi_isl_406592_Guandong_20200113_null_1":{
"Global MG94xREV":0.001718633592991756,
"Nucleotide GTR":0.001687880197520435,
"original name":"epi_isl_406592_Guandong_20200113_null_1"
},
"epi_isl_406799_Wuhan_20191231_null_1":{
"Global MG94xREV":0.01042655806641281,
"Nucleotide GTR":0.01026020645142418,
"original name":"epi_isl_406799_Wuhan_20191231_null_1"
},
"epi_isl_411929_South_Korea_20200101_null_1":{
"Global MG94xREV":0.001717688771578261,
"Nucleotide GTR":0.001685444851869426,
"original name":"epi_isl_411929_South_Korea_20200101_null_1"
},
"epi_isl_413870_Guangdong_20200228_null_1":{
"Global MG94xREV":0.001713725283571032,
"Nucleotide GTR":0.001684815321224942,
"original name":"epi_isl_413870_Guangdong_20200228_null_1"
},
"epi_isl_414008_England_20200227_null_1":{
"Global MG94xREV":0.001715121143755748,
"Nucleotide GTR":0.001684889343264406,
"original name":"epi_isl_414008_England_20200227_null_1"
},
"epi_isl_415537_Wales_20200308_null_1":{
"Global MG94xREV":0.001717147534253156,
"Nucleotide GTR":0.001692869595158266,
"original name":"epi_isl_415537_Wales_20200308_null_1"
},
"epi_isl_417445_Lombardy_20200224_null_1":{
"Global MG94xREV":0.003454440789823345,
"Nucleotide GTR":0.003397382546965385,
"original name":"epi_isl_417445_Lombardy_20200224_null_1"
},
"epi_isl_417554_Reykjavik_20200316_null_2":{
"Global MG94xREV":0.001714809638428961,
"Nucleotide GTR":0.001685656284995428,
"original name":"epi_isl_417554_Reykjavik_20200316_null_2"
},
"epi_isl_417919_Kuala_Lumpur_20200314_null_1":{
"Global MG94xREV":0.001715379415437473,
"Nucleotide GTR":0.001684833447710259,
"original name":"epi_isl_417919_Kuala_Lumpur_20200314_null_1"
},
"epi_isl_418081_Washington_20200315_null_2":{
"Global MG94xREV":0.001716349654403855,
"Nucleotide GTR":0.001685851049353527,
"original name":"epi_isl_418081_Washington_20200315_null_2"
},
"epi_isl_418307_Derbyshire_20200324_null_2":{
"Global MG94xREV":0.001713942748334268,
"Nucleotide GTR":0.001684815309326239,
"original name":"epi_isl_418307_Derbyshire_20200324_null_2"
},
"epi_isl_418385_Finland_20200313_null_1":{
"Global MG94xREV":0.001713800916935459,
"Nucleotide GTR":0.001684815341560461,
"original name":"epi_isl_418385_Finland_20200313_null_1"
},
"epi_isl_418697_England_20200316_null_2":{
"Global MG94xREV":0.001714898404720777,
"Nucleotide GTR":0.001685444851869426,
"original name":"epi_isl_418697_England_20200316_null_2"
},
"epi_isl_419246_Hong_Kong_20200223_null_1":{
"Global MG94xREV":0.001714655762638374,
"Nucleotide GTR":0.001685656249930653,
"original name":"epi_isl_419246_Hong_Kong_20200223_null_1"
},
"epi_isl_419657_Austria_20200303_null_1":{
"Global MG94xREV":0.0017147575085618,
"Nucleotide GTR":0.001685444851869426,
"original name":"epi_isl_419657_Austria_20200303_null_1"
},
"epi_isl_419986_Victoria_20200323_null_1":{
"Global MG94xREV":0.001716008745787844,
"Nucleotide GTR":0.001685210813199801,
"original name":"epi_isl_419986_Victoria_20200323_null_1"
},
"epi_isl_420031_Kinshasa_20200321_null_1":{
"Global MG94xREV":0.001715375410749097,
"Nucleotide GTR":0.001685851055458166,
"original name":"epi_isl_420031_Kinshasa_20200321_null_1"
},
"epi_isl_420318_Arbre_20200307_null_1":{
"Global MG94xREV":0.001713972134102896,
"Nucleotide GTR":0.001684703875469947,
"original name":"epi_isl_420318_Arbre_20200307_null_1"
},
"epi_isl_420320_Ukkel_20200309_null_1":{
"Global MG94xREV":0.001718823903509086,
"Nucleotide GTR":0.001691833859549989,
"original name":"epi_isl_420320_Ukkel_20200309_null_1"
},
"epi_isl_420388_Vilvoorde_20200324_null_1":{
"Global MG94xREV":0.001712926700954332,
"Nucleotide GTR":0.001684902707725008,
"original name":"epi_isl_420388_Vilvoorde_20200324_null_1"
},
"epi_isl_420498_England_20200322_null_1":{
"Global MG94xREV":0.001714489751657862,
"Nucleotide GTR":0.001685258625529165,
"original name":"epi_isl_420498_England_20200322_null_1"
},
"epi_isl_420640_England_20200323_null_3":{
"Global MG94xREV":0.00171260896120798,
"Nucleotide GTR":0.001684833459767918,
"original name":"epi_isl_420640_England_20200323_null_3"
},
"epi_isl_420701_England_20200327_null_3":{
"Global MG94xREV":0.001717688574685132,
"Nucleotide GTR":0.001685444830136264,
"original name":"epi_isl_420701_England_20200327_null_3"
},
"epi_isl_420805_Utah_20200314_null_4":{
"Global MG94xREV":0.00171471670079855,
"Nucleotide GTR":0.001685110880494488,
"original name":"epi_isl_420805_Utah_20200314_null_4"
},
"epi_isl_421177_Madrid_20200327_null_1":{
"Global MG94xREV":0.001714702736331016,
"Nucleotide GTR":0.001684452772380933,
"original name":"epi_isl_421177_Madrid_20200327_null_1"
},
"epi_isl_421393_New_York_20200318_null_2":{
"Global MG94xREV":0.001715831111437788,
"Nucleotide GTR":0.001685549122982956,
"original name":"epi_isl_421393_New_York_20200318_null_2"
},
"epi_isl_421482_Portugal_20200318_null_1":{
"Global MG94xREV":0.001714509970491858,
"Nucleotide GTR":0.001684311264634788,
"original name":"epi_isl_421482_Portugal_20200318_null_1"
},
"epi_isl_421731_New_York_20200318_null_1":{
"Global MG94xREV":0.001716718377575282,
"Nucleotide GTR":0.001685110880850455,
"original name":"epi_isl_421731_New_York_20200318_null_1"
},
"epi_isl_421789_England_20200325_null_1":{
"Global MG94xREV":0.001715261266610748,
"Nucleotide GTR":0.001685140335946919,
"original name":"epi_isl_421789_England_20200325_null_1"
},
"epi_isl_421980_England_20200331_null_1":{
"Global MG94xREV":0.001715369657417508,
"Nucleotide GTR":0.001685819513574204,
"original name":"epi_isl_421980_England_20200331_null_1"
},
"epi_isl_422115_Wales_20200330_null_2":{
"Global MG94xREV":0.001715271761232263,
"Nucleotide GTR":0.001685656242699786,
"original name":"epi_isl_422115_Wales_20200330_null_2"
},
"epi_isl_422197_Wales_20200329_null_2":{
"Global MG94xREV":0.001712926065558896,
"Nucleotide GTR":0.001684902745610414,
"original name":"epi_isl_422197_Wales_20200329_null_2"
},
"epi_isl_422281_Wales_20200327_null_2":{
"Global MG94xREV":0.001713858399762067,
"Nucleotide GTR":0.001684594579470967,
"original name":"epi_isl_422281_Wales_20200327_null_2"
},
"epi_isl_422600_Netherlands_20200401_null_2":{
"Global MG94xREV":0.001713859217245282,
"Nucleotide GTR":0.001684594534552538,
"original name":"epi_isl_422600_Netherlands_20200401_null_2"
},
"epi_isl_422656_Netherlands_20200318_null_2":{
"Global MG94xREV":0.001715223513211816,
"Nucleotide GTR":0.001684899521893436,
"original name":"epi_isl_422656_Netherlands_20200318_null_2"
},
"epi_isl_422717_Netherlands_20200322_null_5":{
"Global MG94xREV":0.001715194632554045,
"Nucleotide GTR":0.00168489951636281,
"original name":"epi_isl_422717_Netherlands_20200322_null_5"
},
"epi_isl_422958_Zuid_Holland_20200329_null_13":{
"Global MG94xREV":0.001716907286811026,
"Nucleotide GTR":0.001685784138619823,
"original name":"epi_isl_422958_Zuid_Holland_20200329_null_13"
},
"epi_isl_423012_Washington_20200319_null_1":{
"Global MG94xREV":0.001713758490476954,
"Nucleotide GTR":0.001684594582176526,
"original name":"epi_isl_423012_Washington_20200319_null_1"
},
"epi_isl_423085_England_20200325_null_1":{
"Global MG94xREV":0.001715873118665688,
"Nucleotide GTR":0.001685100800291464,
"original name":"epi_isl_423085_England_20200325_null_1"
},
"epi_isl_423389_England_20200330_null_1":{
"Global MG94xREV":0.001716574794067751,
"Nucleotide GTR":0.001685624173325825,
"original name":"epi_isl_423389_England_20200330_null_1"
},
"epi_isl_423898_England_20200318_null_1":{
"Global MG94xREV":0.001715611566803351,
"Nucleotide GTR":0.001685624201477991,
"original name":"epi_isl_423898_England_20200318_null_1"
},
"epi_isl_423992_England_20200321_null_1":{
"Global MG94xREV":0.001713502263197742,
"Nucleotide GTR":0.001684376876684914,
"original name":"epi_isl_423992_England_20200321_null_1"
},
"epi_isl_424018_England_20200312_null_8":{
"Global MG94xREV":0.001715481594712576,
"Nucleotide GTR":0.00168506546523512,
"original name":"epi_isl_424018_England_20200312_null_8"
},
"epi_isl_424090_England_20200313_null_2":{
"Global MG94xREV":0.001717212669207147,
"Nucleotide GTR":0.001685624166934991,
"original name":"epi_isl_424090_England_20200313_null_2"
},
"epi_isl_424171_Washington_20200319_null_1":{
"Global MG94xREV":0.005188358273036515,
"Nucleotide GTR":0.005092290254076159,
"original name":"epi_isl_424171_Washington_20200319_null_1"
},
"epi_isl_424210_Washington_20200320_null_1":{
"Global MG94xREV":0.001714346624002774,
"Nucleotide GTR":0.001684899507112928,
"original name":"epi_isl_424210_Washington_20200320_null_1"
},
"epi_isl_424325_Washington_20200324_null_3":{
"Global MG94xREV":0.001715270795921032,
"Nucleotide GTR":0.001685065461536785,
"original name":"epi_isl_424325_Washington_20200324_null_3"
},
"epi_isl_424348_Mexico_City_20200313_null_1":{
"Global MG94xREV":0.001716549051569213,
"Nucleotide GTR":0.001684899507733029,
"original name":"epi_isl_424348_Mexico_City_20200313_null_1"
},
"epi_isl_424485_Reykjavik_20200320_null_5":{
"Global MG94xREV":0.001715194632784696,
"Nucleotide GTR":0.001684899516587901,
"original name":"epi_isl_424485_Reykjavik_20200320_null_5"
},
"epi_isl_424636_Li_ge_20200403_null_1":{
"Global MG94xREV":0.001715554148299391,
"Nucleotide GTR":0.001684899513061833,
"original name":"epi_isl_424636_Li_ge_20200403_null_1"
},
"epi_isl_425440_England_20200101_null_2":{
"Global MG94xREV":0.001713783579015519,
"Nucleotide GTR":0.001684594515113513,
"original name":"epi_isl_425440_England_20200101_null_2"
},
"epi_isl_425707_Scotland_20200317_null_6":{
"Global MG94xREV":0.001714757540045619,
"Nucleotide GTR":0.001685444849659206,
"original name":"epi_isl_425707_Scotland_20200317_null_6"
},
"epi_isl_426025_New_York_20200303_null_1":{
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"Nucleotide GTR":0.001685444852124368,
"original name":"epi_isl_426025_New_York_20200303_null_1"
},
"epi_isl_426028_New_York_20200304_null_2":{
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"Nucleotide GTR":0.001685444896299128,
"original name":"epi_isl_426028_New_York_20200304_null_2"
},
"epi_isl_426787_Victoria_20200323_null_2":{
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"Nucleotide GTR":0.001685035643539688,
"original name":"epi_isl_426787_Victoria_20200323_null_2"
},
"epi_isl_426843_Victoria_20200324_null_4":{
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"Nucleotide GTR":0.001686057050363036,
"original name":"epi_isl_426843_Victoria_20200324_null_4"
},
"epi_isl_426867_Victoria_20200326_null_1":{
"Global MG94xREV":0.001716060053625216,
"Nucleotide GTR":0.001685858301945693,
"original name":"epi_isl_426867_Victoria_20200326_null_1"
},
"epi_isl_427002_Victoria_20200327_null_2":{
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"Nucleotide GTR":0.001685444896299128,
"original name":"epi_isl_427002_Victoria_20200327_null_2"
},
"epi_isl_427082_Victoria_20200328_null_1":{
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"Nucleotide GTR":0.001685444862219307,
"original name":"epi_isl_427082_Victoria_20200328_null_1"
},
"epi_isl_427091_Victoria_20200403_null_2":{
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"Nucleotide GTR":0.001685624185566673,
"original name":"epi_isl_427091_Victoria_20200403_null_2"
},
"epi_isl_427123_Victoria_20200405_null_10":{
"Global MG94xREV":0.001712609184694111,
"Nucleotide GTR":0.001684833451514509,
"original name":"epi_isl_427123_Victoria_20200405_null_10"
},
"epi_isl_427245_Washington_20200401_null_3":{
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"Nucleotide GTR":0.001685444871570997,
"original name":"epi_isl_427245_Washington_20200401_null_3"
},
"epi_isl_427305_Santa_Catarina_20200310_null_1":{
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"Nucleotide GTR":0.001685444903949946,
"original name":"epi_isl_427305_Santa_Catarina_20200310_null_1"
},
"epi_isl_427387_Liege_20200407_null_2":{
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"Nucleotide GTR":0.001685444894761085,
"original name":"epi_isl_427387_Liege_20200407_null_2"
},
"epi_isl_427480_New_York_20200401_null_1":{
"Global MG94xREV":0.001716306357211144,
"Nucleotide GTR":0.001685851075817042,
"original name":"epi_isl_427480_New_York_20200401_null_1"
},
"epi_isl_427481_New_York_20200401_null_2":{
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"Nucleotide GTR":0.00168585107688081,
"original name":"epi_isl_427481_New_York_20200401_null_2"
},
"epi_isl_427634_New_York_20200406_null_1":{
"Global MG94xREV":0.001714441006726513,
"Nucleotide GTR":0.001685444881673941,
"original name":"epi_isl_427634_New_York_20200406_null_1"
},
"epi_isl_427674_New_South_Wales_20200322_null_1":{
"Global MG94xREV":0.001716885650168304,
"Nucleotide GTR":0.001685444851869426,
"original name":"epi_isl_427674_New_South_Wales_20200322_null_1"
},
"epi_isl_428347_Ile_De_France_20200323_null_3":{
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"Nucleotide GTR":0.001685444883471996,
"original name":"epi_isl_428347_Ile_De_France_20200323_null_3"
},
"epi_isl_428349_Ile_De_France_20200323_null_2":{
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"Nucleotide GTR":0.001699776026238505,
"original name":"epi_isl_428349_Ile_De_France_20200323_null_2"
},
"epi_isl_428677_Madrid_20200311_null_1":{
"Global MG94xREV":0.001716564071277283,
"Nucleotide GTR":0.001685819489945662,
"original name":"epi_isl_428677_Madrid_20200311_null_1"
},
"epi_isl_428704_Madrid_20200311_null_3":{
"Global MG94xREV":0.001717043652201615,
"Nucleotide GTR":0.001687848116459031,
"original name":"epi_isl_428704_Madrid_20200311_null_3"
},
"epi_isl_428720_Ankara_20200321_null_1":{
"Global MG94xREV":0.001716156874570626,
"Nucleotide GTR":0.001685624165342565,
"original name":"epi_isl_428720_Ankara_20200321_null_1"
},
"epi_isl_428729_Wisconsin_20200402_null_1":{
"Global MG94xREV":0.001713912479938341,
"Nucleotide GTR":0.001684815325690406,
"original name":"epi_isl_428729_Wisconsin_20200402_null_1"
},
"epi_isl_428918_Novosibirsk_Region_20200327_null_5":{
"Global MG94xREV":0.001714757509729142,
"Nucleotide GTR":0.001685444846979112,
"original name":"epi_isl_428918_Novosibirsk_Region_20200327_null_5"
},
"epi_isl_429013_California_20200328_null_2":{
"Global MG94xREV":0.001717688577342621,
"Nucleotide GTR":0.001685444832689935,
"original name":"epi_isl_429013_California_20200328_null_2"
},
"epi_isl_429023_California_20200331_null_2":{
"Global MG94xREV":0.001715560118990028,
"Nucleotide GTR":0.001685851049348418,
"original name":"epi_isl_429023_California_20200331_null_2"
},
"epi_isl_429470_Unknown_20200323_null_1":{
"Global MG94xREV":0.001716883565391085,
"Nucleotide GTR":0.001685656265011196,
"original name":"epi_isl_429470_Unknown_20200323_null_1"
},
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},
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},
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"original name":"epi_isl_430132_Washington_20200317_null_20"
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"epi_isl_430354_New_York_20200403_null_9":{
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"original name":"epi_isl_430354_New_York_20200403_null_9"
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"epi_isl_430399_New_York_20200410_null_8":{
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"original name":"epi_isl_430399_New_York_20200410_null_8"
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"epi_isl_430482_Victoria_20200331_null_3":{
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"original name":"epi_isl_430482_Victoria_20200331_null_3"
},
"epi_isl_430593_Victoria_20200408_null_3":{
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"original name":"epi_isl_430593_Victoria_20200408_null_3"
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"epi_isl_430803_Ciudad_Autonoma_de_Buenos_Aires_20200401_null_6":{
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"original name":"epi_isl_430803_Ciudad_Autonoma_de_Buenos_Aires_20200401_null_6"
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"epi_isl_430849_Halland_20200311_null_1":{
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"original name":"epi_isl_430849_Halland_20200311_null_1"
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"epi_isl_430909_USA_20200408_null_1":{
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"original name":"epi_isl_430909_USA_20200408_null_1"
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"epi_isl_430916_USA_20200407_null_3":{
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"Nucleotide GTR":0.001686026198907489,
"original name":"epi_isl_430916_USA_20200407_null_3"
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"epi_isl_431011_Kinshasa_20200407_null_14969":{
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"original name":"epi_isl_431011_Kinshasa_20200407_null_14969"
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"epi_isl_432385_Wales_20200401_null_1":{
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"Nucleotide GTR":0.001685656251091623,
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"epi_isl_432600_England_20200329_null_1":{
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"original name":"epi_isl_432600_England_20200329_null_1"
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"epi_isl_433057_England_20200404_null_1":{
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"Nucleotide GTR":0.0016853090478841,
"original name":"epi_isl_433057_England_20200404_null_1"
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"epi_isl_433296_Scotland_20200323_null_1":{
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"original name":"epi_isl_433296_Scotland_20200323_null_1"
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"epi_isl_433360_Scotland_20200328_null_1":{
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"Nucleotide GTR":0.001685851085345105,
"original name":"epi_isl_433360_Scotland_20200328_null_1"
},
"epi_isl_433576_Scotland_20200402_null_2":{
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"Nucleotide GTR":0.001684815329196078,
"original name":"epi_isl_433576_Scotland_20200402_null_2"
},
"epi_isl_434248_Washington_20200401_null_1":{
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"Nucleotide GTR":0.001685851048291153,
"original name":"epi_isl_434248_Washington_20200401_null_1"
},
"epi_isl_434249_Washington_20200402_null_1":{
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"Nucleotide GTR":0.001685851080162184,
"original name":"epi_isl_434249_Washington_20200402_null_1"
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"epi_isl_434385_Antwerp_20200411_null_1":{
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"Nucleotide GTR":0.001685444851869426,
"original name":"epi_isl_434385_Antwerp_20200411_null_1"
},
"epi_isl_434632_Occitanie_20200409_null_1":{
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"Nucleotide GTR":0.001685444827434227,
"original name":"epi_isl_434632_Occitanie_20200409_null_1"
},
"epi_isl_434666_Vasterbotten_20200408_null_1":{
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"Nucleotide GTR":0.001685656275064667,
"original name":"epi_isl_434666_Vasterbotten_20200408_null_1"
}
},
"attributes":{
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"EBF site 100 (partition 1)":{
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"EBF site 101 (partition 1)":{
"attribute type":"branch label",
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"EBF site 102 (partition 1)":{
"attribute type":"branch label",
"display order":104
},
"EBF site 103 (partition 1)":{
"attribute type":"branch label",
"display order":105
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"EBF site 104 (partition 1)":{
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"EBF site 105 (partition 1)":{
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"EBF site 107 (partition 1)":{
"attribute type":"branch label",
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"EBF site 108 (partition 1)":{
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"EBF site 109 (partition 1)":{
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"EBF site 116 (partition 1)":{
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"EBF site 121 (partition 1)":{
"attribute type":"branch label",
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"EBF site 123 (partition 1)":{
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"EBF site 126 (partition 1)":{
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"EBF site 128 (partition 1)":{
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"EBF site 129 (partition 1)":{
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"EBF site 131 (partition 1)":{
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"EBF site 133 (partition 1)":{
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"EBF site 134 (partition 1)":{
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"EBF site 14 (partition 1)":{
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"EBF site 141 (partition 1)":{
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"display order":143
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"EBF site 144 (partition 1)":{
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"EBF site 145 (partition 1)":{
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"EBF site 146 (partition 1)":{
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"EBF site 147 (partition 1)":{
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"EBF site 148 (partition 1)":{
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"EBF site 15 (partition 1)":{
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"EBF site 152 (partition 1)":{
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"EBF site 153 (partition 1)":{
"attribute type":"branch label",
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"EBF site 154 (partition 1)":{
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"EBF site 155 (partition 1)":{
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"EBF site 158 (partition 1)":{
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"EBF site 159 (partition 1)":{
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"EBF site 16 (partition 1)":{
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"EBF site 160 (partition 1)":{
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"EBF site 169 (partition 1)":{
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"EBF site 17 (partition 1)":{
"attribute type":"branch label",
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"EBF site 172 (partition 1)":{
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"EBF site 176 (partition 1)":{
"attribute type":"branch label",
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"EBF site 177 (partition 1)":{
"attribute type":"branch label",
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"EBF site 182 (partition 1)":{
"attribute type":"branch label",
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"EBF site 186 (partition 1)":{
"attribute type":"branch label",
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"EBF site 187 (partition 1)":{
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"EBF site 189 (partition 1)":{
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"EBF site 19 (partition 1)":{
"attribute type":"branch label",
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"EBF site 191 (partition 1)":{
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"EBF site 192 (partition 1)":{
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"EBF site 194 (partition 1)":{
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"EBF site 195 (partition 1)":{
"attribute type":"branch label",
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"EBF site 198 (partition 1)":{
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"EBF site 2 (partition 1)":{
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"EBF site 21 (partition 1)":{
"attribute type":"branch label",
"display order":23
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"EBF site 26 (partition 1)":{
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"EBF site 27 (partition 1)":{
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"EBF site 3 (partition 1)":{
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"EBF site 33 (partition 1)":{
"attribute type":"branch label",
"display order":35
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"EBF site 34 (partition 1)":{
"attribute type":"branch label",
"display order":36
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"EBF site 35 (partition 1)":{
"attribute type":"branch label",
"display order":37
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"EBF site 36 (partition 1)":{
"attribute type":"branch label",
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"EBF site 37 (partition 1)":{
"attribute type":"branch label",
"display order":39
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"EBF site 4 (partition 1)":{
"attribute type":"branch label",
"display order":6
},
"EBF site 41 (partition 1)":{
"attribute type":"branch label",
"display order":43
},
"EBF site 47 (partition 1)":{
"attribute type":"branch label",
"display order":49
},
"EBF site 51 (partition 1)":{
"attribute type":"branch label",
"display order":53
},
"EBF site 53 (partition 1)":{
"attribute type":"branch label",
"display order":55
},
"EBF site 57 (partition 1)":{
"attribute type":"branch label",
"display order":59
},
"EBF site 59 (partition 1)":{
"attribute type":"branch label",
"display order":61
},
"EBF site 61 (partition 1)":{
"attribute type":"branch label",
"display order":63
},
"EBF site 63 (partition 1)":{
"attribute type":"branch label",
"display order":65
},
"EBF site 7 (partition 1)":{
"attribute type":"branch label",
"display order":9
},
"EBF site 72 (partition 1)":{
"attribute type":"branch label",
"display order":74
},
"EBF site 74 (partition 1)":{
"attribute type":"branch label",
"display order":76
},
"EBF site 76 (partition 1)":{
"attribute type":"branch label",
"display order":78
},
"EBF site 77 (partition 1)":{
"attribute type":"branch label",
"display order":79
},
"EBF site 78 (partition 1)":{
"attribute type":"branch label",
"display order":80
},
"EBF site 79 (partition 1)":{
"attribute type":"branch label",
"display order":81
},
"EBF site 8 (partition 1)":{
"attribute type":"branch label",
"display order":10
},
"EBF site 81 (partition 1)":{
"attribute type":"branch label",
"display order":83
},
"EBF site 83 (partition 1)":{
"attribute type":"branch label",
"display order":85
},
"EBF site 85 (partition 1)":{
"attribute type":"branch label",
"display order":87
},
"EBF site 86 (partition 1)":{
"attribute type":"branch label",
"display order":88
},
"EBF site 89 (partition 1)":{
"attribute type":"branch label",
"display order":91
},
"EBF site 9 (partition 1)":{
"attribute type":"branch label",
"display order":11
},
"EBF site 91 (partition 1)":{
"attribute type":"branch label",
"display order":93
},
"EBF site 93 (partition 1)":{
"attribute type":"branch label",
"display order":95
},
"EBF site 95 (partition 1)":{
"attribute type":"branch label",
"display order":97
},
"Global MG94xREV":{
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"display order":1
},
"Nucleotide GTR":{
"attribute type":"branch length",
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},
"original name":{
"attribute type":"node label",
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}
}
},
"data partitions":{
"0":{
"coverage": [
[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197]
],
"name":"meme.filter.default"
}
},
"fits":{
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"Equilibrium frequencies": [
[0.03814058990655009],
[0.01352490888731432],
[0.02397989236844064],
[0.0518808280793833],
[0.02905844503129594],
[0.0103043194250075],
[0.01826973274278217],
[0.03952681892484233],
[0.01036507372269113],
[0.003675524632764485],
[0.006516767382729971],
[0.01409911616874917],
[0.02824324510284562],
[0.01001524406502356],
[0.01775719723688423],
[0.03841794128446285],
[0.01520569029585032],
[0.005392039722615216],
[0.009560177689326007],
[0.02068357636838433],
[0.01158486842252523],
[0.004108072011211085],
[0.007283681205648915],
[0.01575834480861265],
[0.004132293215890474],
[0.001465338878541772],
[0.002598070632747958],
[0.005620961669247749],
[0.01125986879164416],
[0.003992824963201418],
[0.007079346238953171],
[0.01531626328819264],
[0.03588452323313355],
[0.01272489251954375],
[0.02256144980797925],
[0.04881200802426797],
[0.02733959931923329],
[0.009694805211830481],
[0.01718905372669439],
[0.0371887549593662],
[0.009751965811917755],
[0.003458112457136927],
[0.006131291915606685],
[0.01326513467578121],
[0.02657261955190933],
[0.009422829044265002],
[0.01670683537836094],
[0.03614546890777669],
[0.008286094055218293],
[0.03178501420675705],
[0.01780278230587929],
[0.006312985961089139],
[0.01119303095730172],
[0.02421627694823334],
[0.002251826098283306],
[0.003992525784770883],
[0.008637884635162468],
[0.01730334653612839],
[0.006135882688761761],
[0.01087902385796425],
[0.02353691825528636]
],
"Log Likelihood":-1615.930724198802,
"Rate Distributions":{
"non-synonymous/synonymous rate ratio for *background*": [
[0.6577183554770123, 1]
]
},
"display order":1,
"estimated parameters":118
},
"Nucleotide GTR":{
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"Equilibrium frequencies": [
[0.3249476919053223],
[0.1795802275402119],
[0.2035111808552373],
[0.2919608996992284]
],
"Log Likelihood":-1664.498719753798,
"Rate Distributions":{
"Substitution rate from nucleotide A to nucleotide C":0.03743678653123737,
"Substitution rate from nucleotide A to nucleotide G":1,
"Substitution rate from nucleotide A to nucleotide T":0.2317521313848301,
"Substitution rate from nucleotide C to nucleotide G":0.1775758652042667,
"Substitution rate from nucleotide C to nucleotide T":2.016281171695308,
"Substitution rate from nucleotide G to nucleotide T":0.6685698799074486
},
"display order":0,
"estimated parameters":211
}
},
"input":{
"file name":"/data/shares/veg/SARS-CoV-2/SARS-CoV-2/data/fasta/2020-05-01/sequences.nsp8.compressed.fas",
"number of sequences":103,
"number of sites":198,
"partition count":1,
"trees":{
"0":"(epi_isl_432600_England_20200329_null_1,epi_isl_429023_California_20200331_null_2,epi_isl_430803_Ciudad_Autonoma_de_Buenos_Aires_20200401_null_6,epi_isl_406592_Guandong_20200113_null_1,epi_isl_424636_Li_ge_20200403_null_1,epi_isl_417919_Kuala_Lumpur_20200314_null_1,epi_isl_430399_New_York_20200410_null_8,epi_isl_419986_Victoria_20200323_null_1,epi_isl_421393_New_York_20200318_null_2,epi_isl_434632_Occitanie_20200409_null_1,epi_isl_420640_England_20200323_null_3,epi_isl_424018_England_20200312_null_8,epi_isl_430916_USA_20200407_null_3,epi_isl_427245_Washington_20200401_null_3,epi_isl_430228_Washington_20200323_null_1,epi_isl_423992_England_20200321_null_1,epi_isl_421789_England_20200325_null_1,epi_isl_406799_Wuhan_20191231_null_1,epi_isl_431011_Kinshasa_20200407_null_14969,epi_isl_418697_England_20200316_null_2,epi_isl_429627_Washington_20200327_null_2,epi_isl_419246_Hong_Kong_20200223_null_1,epi_isl_424348_Mexico_City_20200313_null_1,epi_isl_427674_New_South_Wales_20200322_null_1,epi_isl_418081_Washington_20200315_null_2,epi_isl_423389_England_20200330_null_1,epi_isl_424325_Washington_20200324_null_3,epi_isl_427123_Victoria_20200405_null_10,epi_isl_427634_New_York_20200406_null_1,epi_isl_422600_Netherlands_20200401_null_2,epi_isl_428349_Ile_De_France_20200323_null_2,epi_isl_433576_Scotland_20200402_null_2,epi_isl_427082_Victoria_20200328_null_1,epi_isl_422197_Wales_20200329_null_2,epi_isl_430909_USA_20200408_null_1,epi_isl_426025_New_York_20200303_null_1,epi_isl_427305_Santa_Catarina_20200310_null_1,epi_isl_422656_Netherlands_20200318_null_2,epi_isl_426843_Victoria_20200324_null_4,epi_isl_418307_Derbyshire_20200324_null_2,epi_isl_421482_Portugal_20200318_null_1,epi_isl_424090_England_20200313_null_2,epi_isl_428677_Madrid_20200311_null_1,epi_isl_434248_Washington_20200401_null_1,epi_isl_428729_Wisconsin_20200402_null_1,epi_isl_430354_New_York_20200403_null_9,epi_isl_420031_Kinshasa_20200321_null_1,epi_isl_420805_Utah_20200314_null_4,epi_isl_432385_Wales_20200401_null_1,epi_isl_420498_England_20200322_null_1,epi_isl_414008_England_20200227_null_1,epi_isl_417445_Lombardy_20200224_null_1,epi_isl_434249_Washington_20200402_null_1,epi_isl_420701_England_20200327_null_3,epi_isl_423898_England_20200318_null_1,epi_isl_426787_Victoria_20200323_null_2,epi_isl_433057_England_20200404_null_1,epi_isl_413870_Guangdong_20200228_null_1,epi_isl_430482_Victoria_20200331_null_3,epi_isl_417554_Reykjavik_20200316_null_2,epi_isl_420388_Vilvoorde_20200324_null_1,epi_isl_428347_Ile_De_France_20200323_null_3,epi_isl_426028_New_York_20200304_null_2,epi_isl_427387_Liege_20200407_null_2,epi_isl_422717_Netherlands_20200322_null_5,epi_isl_428720_Ankara_20200321_null_1,epi_isl_429013_California_20200328_null_2,epi_isl_427480_New_York_20200401_null_1,epi_isl_422958_Zuid_Holland_20200329_null_13,epi_isl_428704_Madrid_20200311_null_3,epi_isl_421731_New_York_20200318_null_1,epi_isl_420318_Arbre_20200307_null_1,epi_isl_419657_Austria_20200303_null_1,epi_isl_429694_Minas_gerais_20200318_null_1,epi_isl_433296_Scotland_20200323_null_1,epi_isl_421177_Madrid_20200327_null_1,epi_isl_418385_Finland_20200313_null_1,epi_isl_430593_Victoria_20200408_null_3,epi_isl_420320_Ukkel_20200309_null_1,epi_isl_424210_Washington_20200320_null_1,epi_isl_434385_Antwerp_20200411_null_1,epi_isl_427481_New_York_20200401_null_2,epi_isl_422281_Wales_20200327_null_2,epi_isl_429470_Unknown_20200323_null_1,epi_isl_428918_Novosibirsk_Region_20200327_null_5,epi_isl_430849_Halland_20200311_null_1,epi_isl_423012_Washington_20200319_null_1,epi_isl_427091_Victoria_20200403_null_2,epi_isl_433360_Scotland_20200328_null_1,epi_isl_427002_Victoria_20200327_null_2,epi_isl_422115_Wales_20200330_null_2,epi_isl_424485_Reykjavik_20200320_null_5,epi_isl_411929_South_Korea_20200101_null_1,epi_isl_415537_Wales_20200308_null_1,epi_isl_423085_England_20200325_null_1,epi_isl_430132_Washington_20200317_null_20,epi_isl_434666_Vasterbotten_20200408_null_1,epi_isl_425440_England_20200101_null_2,epi_isl_425707_Scotland_20200317_null_6,epi_isl_429571_Unknown_20200326_null_1,epi_isl_421980_England_20200331_null_1,epi_isl_424171_Washington_20200319_null_1,epi_isl_426867_Victoria_20200326_null_1)"
}
},
"tested":{
"0":{
"epi_isl_406592_Guandong_20200113_null_1":"background",
"epi_isl_406799_Wuhan_20191231_null_1":"background",
"epi_isl_411929_South_Korea_20200101_null_1":"background",
"epi_isl_413870_Guangdong_20200228_null_1":"background",
"epi_isl_414008_England_20200227_null_1":"background",
"epi_isl_415537_Wales_20200308_null_1":"background",
"epi_isl_417445_Lombardy_20200224_null_1":"background",
"epi_isl_417554_Reykjavik_20200316_null_2":"background",
"epi_isl_417919_Kuala_Lumpur_20200314_null_1":"background",
"epi_isl_418081_Washington_20200315_null_2":"background",
"epi_isl_418307_Derbyshire_20200324_null_2":"background",
"epi_isl_418385_Finland_20200313_null_1":"background",
"epi_isl_418697_England_20200316_null_2":"background",
"epi_isl_419246_Hong_Kong_20200223_null_1":"background",
"epi_isl_419657_Austria_20200303_null_1":"background",
"epi_isl_419986_Victoria_20200323_null_1":"background",
"epi_isl_420031_Kinshasa_20200321_null_1":"background",
"epi_isl_420318_Arbre_20200307_null_1":"background",
"epi_isl_420320_Ukkel_20200309_null_1":"background",
"epi_isl_420388_Vilvoorde_20200324_null_1":"background",
"epi_isl_420498_England_20200322_null_1":"background",
"epi_isl_420640_England_20200323_null_3":"background",
"epi_isl_420701_England_20200327_null_3":"background",
"epi_isl_420805_Utah_20200314_null_4":"background",
"epi_isl_421177_Madrid_20200327_null_1":"background",
"epi_isl_421393_New_York_20200318_null_2":"background",
"epi_isl_421482_Portugal_20200318_null_1":"background",
"epi_isl_421731_New_York_20200318_null_1":"background",
"epi_isl_421789_England_20200325_null_1":"background",
"epi_isl_421980_England_20200331_null_1":"background",
"epi_isl_422115_Wales_20200330_null_2":"background",
"epi_isl_422197_Wales_20200329_null_2":"background",
"epi_isl_422281_Wales_20200327_null_2":"background",
"epi_isl_422600_Netherlands_20200401_null_2":"background",
"epi_isl_422656_Netherlands_20200318_null_2":"background",
"epi_isl_422717_Netherlands_20200322_null_5":"background",
"epi_isl_422958_Zuid_Holland_20200329_null_13":"background",
"epi_isl_423012_Washington_20200319_null_1":"background",
"epi_isl_423085_England_20200325_null_1":"background",
"epi_isl_423389_England_20200330_null_1":"background",
"epi_isl_423898_England_20200318_null_1":"background",
"epi_isl_423992_England_20200321_null_1":"background",
"epi_isl_424018_England_20200312_null_8":"background",
"epi_isl_424090_England_20200313_null_2":"background",
"epi_isl_424171_Washington_20200319_null_1":"background",
"epi_isl_424210_Washington_20200320_null_1":"background",
"epi_isl_424325_Washington_20200324_null_3":"background",
"epi_isl_424348_Mexico_City_20200313_null_1":"background",
"epi_isl_424485_Reykjavik_20200320_null_5":"background",
"epi_isl_424636_Li_ge_20200403_null_1":"background",
"epi_isl_425440_England_20200101_null_2":"background",
"epi_isl_425707_Scotland_20200317_null_6":"background",
"epi_isl_426025_New_York_20200303_null_1":"background",
"epi_isl_426028_New_York_20200304_null_2":"background",
"epi_isl_426787_Victoria_20200323_null_2":"background",
"epi_isl_426843_Victoria_20200324_null_4":"background",
"epi_isl_426867_Victoria_20200326_null_1":"background",
"epi_isl_427002_Victoria_20200327_null_2":"background",
"epi_isl_427082_Victoria_20200328_null_1":"background",
"epi_isl_427091_Victoria_20200403_null_2":"background",
"epi_isl_427123_Victoria_20200405_null_10":"background",
"epi_isl_427245_Washington_20200401_null_3":"background",
"epi_isl_427305_Santa_Catarina_20200310_null_1":"background",
"epi_isl_427387_Liege_20200407_null_2":"background",
"epi_isl_427480_New_York_20200401_null_1":"background",
"epi_isl_427481_New_York_20200401_null_2":"background",
"epi_isl_427634_New_York_20200406_null_1":"background",
"epi_isl_427674_New_South_Wales_20200322_null_1":"background",
"epi_isl_428347_Ile_De_France_20200323_null_3":"background",
"epi_isl_428349_Ile_De_France_20200323_null_2":"background",
"epi_isl_428677_Madrid_20200311_null_1":"background",
"epi_isl_428704_Madrid_20200311_null_3":"background",
"epi_isl_428720_Ankara_20200321_null_1":"background",
"epi_isl_428729_Wisconsin_20200402_null_1":"background",
"epi_isl_428918_Novosibirsk_Region_20200327_null_5":"background",
"epi_isl_429013_California_20200328_null_2":"background",
"epi_isl_429023_California_20200331_null_2":"background",
"epi_isl_429470_Unknown_20200323_null_1":"background",
"epi_isl_429571_Unknown_20200326_null_1":"background",
"epi_isl_429627_Washington_20200327_null_2":"background",
"epi_isl_429694_Minas_gerais_20200318_null_1":"background",
"epi_isl_430132_Washington_20200317_null_20":"background",
"epi_isl_430228_Washington_20200323_null_1":"background",
"epi_isl_430354_New_York_20200403_null_9":"background",
"epi_isl_430399_New_York_20200410_null_8":"background",
"epi_isl_430482_Victoria_20200331_null_3":"background",
"epi_isl_430593_Victoria_20200408_null_3":"background",
"epi_isl_430803_Ciudad_Autonoma_de_Buenos_Aires_20200401_null_6":"background",
"epi_isl_430849_Halland_20200311_null_1":"background",
"epi_isl_430909_USA_20200408_null_1":"background",
"epi_isl_430916_USA_20200407_null_3":"background",
"epi_isl_431011_Kinshasa_20200407_null_14969":"background",
"epi_isl_432385_Wales_20200401_null_1":"background",
"epi_isl_432600_England_20200329_null_1":"background",
"epi_isl_433057_England_20200404_null_1":"background",
"epi_isl_433296_Scotland_20200323_null_1":"background",
"epi_isl_433360_Scotland_20200328_null_1":"background",
"epi_isl_433576_Scotland_20200402_null_2":"background",
"epi_isl_434248_Washington_20200401_null_1":"background",
"epi_isl_434249_Washington_20200402_null_1":"background",
"epi_isl_434385_Antwerp_20200411_null_1":"background",
"epi_isl_434632_Occitanie_20200409_null_1":"background",
"epi_isl_434666_Vasterbotten_20200408_null_1":"background"
}
},
"timers":{
"MEME analysis":{
"order":2,
"timer":22
},
"Model fitting":{
"order":1,
"timer":9
},
"Total time":{
"order":0,
"timer":33
}
}
}